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<title>GenomeTools - manual page for GT-SHREDDER(1)</title>
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<div class="sect1">
<h2 id="_name">NAME</h2>
<div class="sectionbody">
<div class="paragraph"><p>gt-shredder - Shredder sequence file(s) into consecutive pieces of random length.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_synopsis">SYNOPSIS</h2>
<div class="sectionbody">
<div class="paragraph"><p><strong>gt shredder</strong> [option &#8230;] [sequence_file &#8230;]</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_description">DESCRIPTION</h2>
<div class="sectionbody">
<div class="dlist"><dl>
<dt class="hdlist1">
<strong>-coverage</strong> [<em>value</em>]
</dt>
<dd>
<p>
set the number of times the sequence_file is shreddered (default: 1)
</p>
</dd>
<dt class="hdlist1">
<strong>-minlength</strong> [<em>value</em>]
</dt>
<dd>
<p>
set the minimum length of the shreddered fragments (default: 300)
</p>
</dd>
<dt class="hdlist1">
<strong>-maxlength</strong> [<em>value</em>]
</dt>
<dd>
<p>
set the maximum length of the shreddered fragments (default: 700)
</p>
</dd>
<dt class="hdlist1">
<strong>-overlap</strong> [<em>value</em>]
</dt>
<dd>
<p>
set the overlap between consecutive pieces (default: 0)
</p>
</dd>
<dt class="hdlist1">
<strong>-sample</strong> [<em>value</em>]
</dt>
<dd>
<p>
take samples of the generated sequences pieces with the given probability (default: 1.000000)
</p>
</dd>
<dt class="hdlist1">
<strong>-clipdesc</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
clip descriptions after first space (fooled by <em>\t</em>, <em>\n</em> etc) adds offset and length to ensure unique identifier (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-width</strong> [<em>value</em>]
</dt>
<dd>
<p>
set output width for FASTA sequence printing
(0 disables formatting) (default: 0)
</p>
</dd>
<dt class="hdlist1">
<strong>-o</strong> [<em>filename</em>]
</dt>
<dd>
<p>
redirect output to specified file (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-gzip</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
write gzip compressed output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-bzip2</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
write bzip2 compressed output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-force</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
force writing to output file (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-help</strong> 
</dt>
<dd>
<p>
display help and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-version</strong> 
</dt>
<dd>
<p>
display version information and exit
</p>
</dd>
</dl></div>
<div class="paragraph"><p>Each sequence given in <em>sequence_file</em> is shreddered into consecutive pieces of
random length (between <em>-minlength</em> and <em>-maxlength</em>) until it is consumed.
By this means the last shreddered fragment of a given sequence can be shorter
than the argument to option <em>-minlength</em>.
To get rid of such fragments use <tt>gt seqfilter</tt> (see example below).</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_examples">Examples:</h2>
<div class="sectionbody">
<div class="paragraph"><p>Shredder a given BAC:</p></div>
<div class="literalblock">
<div class="content">
<pre><tt>$ gt shredder U89959_genomic.fas &gt; fragments.fas</tt></pre>
</div></div>
<div class="paragraph"><p>Shredder an EST collection into pieces between 50 and 100 bp and get rid of all
(terminal) fragments shorter than 50 bp:</p></div>
<div class="literalblock">
<div class="content">
<pre><tt>$ gt shredder -minlength 50 -maxlength 100 U89959_ests.fas \
  | gt seqfilter -minlength 50 - &gt; fragments.fas
# 130 out of 1260 sequences have been removed (10.317%)</tt></pre>
</div></div>
<div class="paragraph"><p>Shredder an EST collection and show only random 10% of the resulting fragments:</p></div>
<div class="literalblock">
<div class="content">
<pre><tt>$ gt shredder -sample 0.1 U89959_ests.fas</tt></pre>
</div></div>
</div>
</div>
<div class="sect1">
<h2 id="_reporting_bugs">REPORTING BUGS</h2>
<div class="sectionbody">
<div class="paragraph"><p>Report bugs to <a href="https://github.com/genometools/genometools/issues">https://github.com/genometools/genometools/issues</a>.</p></div>
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